Captive animal populations can diverge considerably from populations in the wild, despite the animals not being deliberately domesticated. If the phenotypes which are of benefit in captivity are heritable, the genotypes of captive-stock can diverge swiftly and substantially from wild-stock. Using striped mice, Rhabdomys, we tested the relationship between reproductive output and stereotypic behaviour, a heritable repetitive abnormal behaviour common in captive wild animals. Individuals (n = 120; 60 males, 60 females) were assigned to pairs in one of four treatment groups formed from combinations of non-stereotypic and stereotypic mothers and fathers, and various measures of reproductive output were recorded. Reproductive output (e.g. total number of offspring) for stereotypic females (but not stereotypic males) was significantly greater than for non-stereotypic striped mice. We suggest that, overall, unintended selection is likely to increase the incidence of stereotypic behaviour in a captive striped mouse population because (1) stereotypic females breed more successfully than non-stereotypic striped mice, and (2) genetic variance underlies the trait. The potential implications of these findings for the validity of behavioural studies using captive-bred wild animals and for conservation breeding programmes are discussed.